Please help me figure out what got newly hatched chicks

I had a little bantam OEG hen sitting on eggs in her run. She made a secret nest outside of her nest box. I had been keeping an eye on her. She is alone besides her devoted roo. He always takes very good care of her. Anyway, this morning I checked and she was off the nest looking very distraut. There were shells around that look like after a chick hatches (top zipped open, but still attached). I can't figure out what got the chicks. The run is cat proof, dog proof - I've had racoons pull large chickens heads off through the run, but none have ever gotten into it. We've had snakes before too (they were, er, eliminated), but they always ate the eggs. I can't imagine one waiting around for the chicks to hatch unless it was just good timing on their part. I am just sick about this. We had just hatched some of her eggs in the incubator - they are one week old, when we found she was brooding. I wish I had moved her to a safer place, but I was afraid she would freak out and stop brooding. Any ideas? There were no chick parts left behind, just the shells - no blood, feathers, etc. Thanks everyone.

Nothing can fly into the run. It is totally enclosed on top with the bottom of the fencing buried about 8 inches.

I was hoping she had hid the chicks, but she seemed very upset. There are plenty of hiding places in the run, so they could be hidden, but I thought they would make some noise and I expected her to have them gathered around her. Haven't seen any marks of snakes, but not sure I'd be able to anyway. I hope it wasn't a snake - you just can't keep them out once they decide to come in.

She had been sitting on about 10 eggs. Very dilligent, camoflauged so well, you could barely see her.

The rooster would not come out of the coop this morning when I was out there. Usually he comes running up and tries to scare me off. He's always been very protective of her. So that was odd.

I have never seen live rats at our place, but I have seen dead ones killed by our barn cats. So if rats are a possibility, then that could be what got them.

We are on ten acres with a pond and branch head of a creek running across back of land. Everything is there - foxes, bobcats, etc. That's why the run and coop are made so most things can not get in. We keep the chickens near the house so I can hear problems and some predators don't like to come to close to dogs/cats. Problem is, I didn't get home until late last night and checked hen this morning. Something could have happened before I got home. We have another coop with RIR and BO. They free range and are locked up at night. Only time they weren't locked in at night was the only time racoons were able to kill two of them.

Rooster would not come out of his coop this am. I had to go to work and I have not seen him, although I heard him crowing. I'll check again when I get home.